Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh

Abstract Radish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks rel...

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Autores principales:	Jifang Zhang, Jian Zhao, Qunyun Tan, Xiaojun Qiu, Shiyong Mei
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8aae98e03fe341958cb55d3836379015
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spelling	oai:doaj.org-article:8aae98e03fe341958cb55d38363790152021-12-02T17:51:13ZComparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh10.1038/s41598-021-90633-52045-2322https://doaj.org/article/8aae98e03fe341958cb55d38363790152021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-90633-5https://doaj.org/toc/2045-2322Abstract Radish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (RsTT4, RsC4H, RsTT7, RsCCOAMT, RsDFR, and RsLDOX) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (RsTT4, RsDFR, RsCCOAMT, RsF3H, and RsBG8L) and three transcription factors (RsTT8-1, RsTT8-2, and RsPAR1) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (RsBG8L, RsDFR, RsCCOAMT, and RsLDOX) and nine transcription factors (RsTT8-1, RsTT8-2, RsMYB24L, RsbHLH57, RsPAR2L, RsbHLH113L, RsOGR3L, RsMYB24, and RsMYB34L) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.Jifang ZhangJian ZhaoQunyun TanXiaojun QiuShiyong MeiNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jifang Zhang Jian Zhao Qunyun Tan Xiaojun Qiu Shiyong Mei Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh
description	Abstract Radish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (RsTT4, RsC4H, RsTT7, RsCCOAMT, RsDFR, and RsLDOX) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (RsTT4, RsDFR, RsCCOAMT, RsF3H, and RsBG8L) and three transcription factors (RsTT8-1, RsTT8-2, and RsPAR1) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (RsBG8L, RsDFR, RsCCOAMT, and RsLDOX) and nine transcription factors (RsTT8-1, RsTT8-2, RsMYB24L, RsbHLH57, RsPAR2L, RsbHLH113L, RsOGR3L, RsMYB24, and RsMYB34L) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.
format	article
author	Jifang Zhang Jian Zhao Qunyun Tan Xiaojun Qiu Shiyong Mei
author_facet	Jifang Zhang Jian Zhao Qunyun Tan Xiaojun Qiu Shiyong Mei
author_sort	Jifang Zhang
title	Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh
title_short	Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh
title_full	Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh
title_fullStr	Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh
title_full_unstemmed	Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh
title_sort	comparative transcriptome analysis reveals key genes associated with pigmentation in radish (raphanus sativus l.) skin and flesh
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/8aae98e03fe341958cb55d3836379015
work_keys_str_mv	AT jifangzhang comparativetranscriptomeanalysisrevealskeygenesassociatedwithpigmentationinradishraphanussativuslskinandflesh AT jianzhao comparativetranscriptomeanalysisrevealskeygenesassociatedwithpigmentationinradishraphanussativuslskinandflesh AT qunyuntan comparativetranscriptomeanalysisrevealskeygenesassociatedwithpigmentationinradishraphanussativuslskinandflesh AT xiaojunqiu comparativetranscriptomeanalysisrevealskeygenesassociatedwithpigmentationinradishraphanussativuslskinandflesh AT shiyongmei comparativetranscriptomeanalysisrevealskeygenesassociatedwithpigmentationinradishraphanussativuslskinandflesh
_version_	1718379296565755904

Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh

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